Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

Cell type

Cell type Class
Epidermis
Cell type
Keratinocytes
MeSH Description
Epidermal cells which synthesize keratin and undergo characteristic changes as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.

Attributes by original data submitter

Sample

source_name
epidermal keratinocytes from foreskin
cell type
epidermal keratinocytes
chip antibody
MED1, Bethyl A300-793A, lot A300-793A-8

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
When keratinocytes are under pre-confluency, they were cross-linked by 1% paraformaldehyde for 8 min for H3K27ac and for 15 min for MED1/CTCF and quenched with 0.125M glycine. Whole cell lysates (for H3K27ac) or purified chromatin (MED1/CTCF) were sonicated by Covaris S2200 ultrasonicator (Covaris, Inc.). The shearing condition was optimized to obtain the DNA to an average length of 300±50 bp, in which size of DNA was verified by Agilent 2100 Bioanalyzer (Agilent Technologies). Sheared chromatin was immunoprecipitated with Protein A-coated magnetic beads (Diagenode) preincubated with antibodies: 3 ug of antibody against H3K27ac (ab4729, Abcam), 1 ug CTCF antibody (Diagenode) and 4.5 ug MED1 antibody (Bethyl). Experiments were carried out in replicates (2-3), and a chromatin input sample was used as a reference to subtract background for peak calling. Complexes were washed, eluted from the beads with washing buffer and crosslinks were reversed by incubation at 65C for 4 hr. Immunoprecipitated DNA along with genomic DNA (Input) were purified using IPure v2 kit (Diagenode). IP efficiency was confirmed by qPCR using primers provided in the kits. DNA Sequencing libraries were generated using the Accel-NGS 2S Plus DNA library kits (Swift Sciences) and amplified by PCR for 11 cycles. To remove high MW smear in the library, right side size selection was conducted by using SPRI beads (Beckman Coulter). The library was quantified by Agilent 2100 Bioanalyzer with the High sensitivity DNA assay. They were sequenced on an Illumina HiSeq 4000 (UCSF Center of advanced technology) in a single strand 50bp run (combining 8 libraries per lane).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
70207574
Reads aligned (%)
98.9
Duplicates removed (%)
8.0
Number of peaks
9088 (qval < 1E-05)

hg19

Number of total reads
70207574
Reads aligned (%)
98.5
Duplicates removed (%)
8.4
Number of peaks
9086 (qval < 1E-05)

Base call quality data from DBCLS SRA